We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
VariantAnnotator and Mutect2
Dear Sheila, and Geraldine,
continuing our previous conversation about the fields in the VCF file produced by MUTECT2, please could you advise on why I see the following DIFFERENCES :
-- shall I run MUTECT2 with the options -A for FS, MQ, SOR, I am getting the following numerical values for a chr position :
FS=2.433; MQ=45.70; MQRankSum=-3.331 ; ReadPosRankSum=-0.654; SOR=1.489
-- shall I run MUTECT2 with NO -A options, but using VariantAnnotator on the VCF file in order to add FS, MQ, and SOR, the numerical values are :
FS=0.000; MQ=33.87; SOR=2.636;
the question would be of course, why these numerical values differ ? many thanks,